So, I heard back from Ford. Their response letter 100% useless just as I figured.
"Because we do not have any information in our system that differentiates the towing capabilities between the 2 transmissions (auto VS manual), I am unable to advise if the abilities change based on the type." So, given that honestly it sounds as though Ford just has no idea, which they're the ones that designed and built it you'd think they could answer that question with a logical explanation, but what do you expect from an automaker these days.
The letter further goes on stating everything we already know that vehicle options, engines, etc. all play a role in towing capacity. That aside, why can't my 87 Ranger 2.9L V6, 4x2 long bed 5 speed with 3.73 gear ratio tow the same trailer an 87 Ranger 2.9L V6 4x2 long bed with the automatic and 3.73 axle ratio can tow. They completely left out the answer. So with the response I got I'd think both trucks could tow the same thing being equipped the same. The weight of the vehicle plays a factor in how much it can tow, well if that's the case the same Ranger equipped the same just an auto vs manual wouldn't weigh that much different overall, so why would you be able to tow a 5k pound trailer behind the auto vs 2k pound trailer behind the manual...I mean other than the way people drive they'd smoke the clutch right out of the manual. Aside from that, you get a person that knows how to drive there's no honest reason you couldn't tow the same trailer with either truck. Some have mentioned the way the gears are cut and mesh in a manual, well that logic should be the same behind a 1 ton dually manual then as well, or a semi-truck for that matter. People have been towing for decades with manuals just fine, so really is the truth actually in the loose nut behind the wheel being the real reason? I'd have to think so. Given when you push that clutch pedal in you just disconnected the drive wheels from the engine, now you have no engine braking, and no connection to the ground, so, someone with less than good driving skills on a hill may end up not ending up where they intended to go as that trailer pushes them down the hill for example. I'd have to think that would make more logical sense overall then the way the gears are between a manual and automatic if you have a good driver they should be able to tow the same weight regardless which transmission is there.